Abstract

Published genome-wide association studies (GWASs) have identified few variants in the known biological pathways involved in lung cancer etiology. To mine the possibly hidden causal single nucleotide polymorphisms (SNPs), we explored all SNPs in the extrinsic apoptosis pathway from our published GWAS dataset for 1154 lung cancer cases and 1137 cancer-free controls. In an initial association analysis of 611 tagSNPs in 41 apoptosis-related genes, we identified only 10 tagSNPs associated with lung cancer risk with a P value<10(-2), including four tagSNPs in DAPK1 and three tagSNPs in TNFSF8. Unlike DAPK1 SNPs, TNFSF8 rs2181033 tagged other four predicted functional but untyped SNPs (rs776576, rs776577, rs31813148 and rs2075533) in the promoter region. Therefore, we further tested binding affinity of these four SNPs by performing the electrophoretic mobility shift assay. We found that only rs2075533T allele modified levels of nuclear proteins bound to DNA, leading to significantly decreased expression of luciferase reporter constructs by 5- to -10-fold in H1299, HeLa and HCT116 cell lines compared with the C allele. We also performed a replication study of the untyped rs2075533 in an independent Texas population but did not confirm the protective effect. We further performed a mini meta-analysis for SNPs of TNFSF8 obtained from other four published lung cancer GWASs with 12 214 cases and 47 721 controls, and we found that only rs3181366 (r2=0.69 with the untyped rs2075533) was associated to lung cancer risk (P=0.008). Our findings suggest a possible role of novel TNFSF8 variants in susceptibility to lung cancer.

Association between genetic variants of DAPK1 and TNFSF8 and lung cancer risk based on the data from the Texas lung cancer GWAS. (A) A total of 92 SNPs were assigned to DAPK1, which covered the gene region between 89 175 300 and 89 347 200 bp on chromosome 9. Only four SNPs had a P value <0.01 and two SNPs rs3128477 and rs721936 were in high LD (r2 = 0.99). LD patterns among these SNPs were inferred in the control subjects by Haploview. (B) A total of 18 SNPs were assigned to TNFSF8, which covered the gene region between 116 660 000 and 116 780 000 bp on chromosome 9. Only three SNPs had a P value <0.01 and three SNPs were in high LD to each other (r2 > 0.8). LD patterns among these SNPs were inferred in the control subjects by Haploview.

Meta-analysis for the five top significant SNPs in TNFSF8 based on fixed effect, dominant model using genotypes data from deCODE, National Cancer Institute, IARC, Texas lung cancer GWAS and Texas replication study.